Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT

Basic information

species Vitis vinifera
transcript Vv08s0007g04700.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------------tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
                                                                                               | ||  |||       | |   |  ||||| | |  || |   | |  |   |   ||   ||||   ||||| |||    |||||      ||| |||||||| || |||||||| ||||||||||| || ||||| ||||| ||||| || ||||||  |||||| ||| |||| ||||| ||||| || ||||| 
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatacttt---aaaacacaata--ttgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 3
------tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
      || | |  | |       | |   || |||| || |  |  |   | |  |  |||  |  || ||    ||||| || ||        | |  ||| |||||||| || |||||||| ||||||||||| || ||||| ||||| ||||| ||||||||   |||||| ||| |||| ||||| ||||| || ||||| 
tcttgttgacatattcttgttgtttctcctgacttaatttataatgttctttctgttccagactcgtacttt----aaaacaca-gtatcaatccaatc-ttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGCGGAAACTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 2
tgtcttgatttaccaaaat-tta--tagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactca-----agtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
       |   || | ||| |||  | |  ||  |  |  ||  |   | ||| |    |||      ||    ||  | |     | | ||||  ||    | | || ||||| ||||||||||| ||||||||||| || || || ||| | |||||||| |||| ||| || || ||||| || ||||||||||| || ||||| 
-------aacgacgagaatgttaccttgttttgcacctgattggtgcctctacctgtactgctttgtatttcagaatttaataagaactacttgtgtatctgt-gtagAAATTTGAGGGAGATGTTCAAGATTGATGCAGCGGATTATATGGTTTCCATTTGTGGAAGTGACGCACTTAGGGAGCTATCTTCTCCTGGAAAGAGTGGA

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
tgtcttgatttacca--aaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
 ||   ||  |||    | ||        ||   || | |   ||    | |||    |  |||  |   ||  |  |  |   | |  | ||   ||| || ||||| || ||| |||| ||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatat--atgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
--tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
    |  | |   ||||   ||            |||| ||   |  | | |||    |   ||  |   ||     |  |   | |  | |    ||| || ||||| || ||| |||| ||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtat--atgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
tgtcttgatttaccaaaatttataga--attaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
|||  | ||  || ||   ||| ||   ||     | |  |  ||  |    | |   | || |  ||| | | |  | |  | || ||   ||| ||| || ||||| || ||| |||| ||||||||||| || || ||||||||||||||||| ||||| ||| ||||||||||||| |||||||| ||||||||||||
tgttcttatagac-aactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctg-ttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT

upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtcttgatttaccaaaatttatagaat---taaattttgttaattaatgtacttaagat-gcacacct-ttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
              | || || |  | |   ||  ||||  | | || | |  | |  || | |    | | ||      | |  | | |   ||    ||| || ||  | ||||||||||| ||||| ||||| ||||| || |||||||||||||| ||||||||| || | || |||||||||||||| ||||| || || 
-----------gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
                                           tactgat  putative branch site (score: 2)
     ttaagat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT

tgtcttg
- - - - - taccaaa
- - - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg